SC Controls RNA-Seq
Libraries required for data analysis and plotting
All samples
Most 500 variable genes
Correlation
Computation
Reduced dimensionality representation
PCA Tools
## -- removing the lower 10% of variables based on variance
pscree <- screeplot(p,
components = getComponents(p, 1:20),
hline = 80, vline = 2.6, axisLabSize = 10, returnPlot = FALSE
) +
geom_text(aes(6.5, 80, label = "80% explained variation", vjust = -1))
ppairs <- pairsplot(p,
components = getComponents(p, c(1:3)),
triangle = TRUE, trianglelabSize = 12,
hline = 0, vline = 0,
pointSize = 0.8, gridlines.major = FALSE, gridlines.minor = FALSE,
colby = "Group",
title = "", titleLabSize = 16, plotaxes = FALSE,
margingaps = unit(c(0.01, 0.01, 0.01, 0.01), "cm"),
returnPlot = FALSE
)
pbiplot <- biplot(p,
lab = FALSE,
colby = "Group",
hline = 0, vline = c(-25, 0, 25), vlineType = c("dotdash", "solid", "dashed"),
gridlines.major = FALSE, gridlines.minor = FALSE,
pointSize = 2, axisLabSize = 12,
legendPosition = "left", legendLabSize = 10, legendIconSize = 3.0,
drawConnectors = FALSE,
title = "PCA bi-plot", subtitle = "PC1 versus PC2",
caption = "2 PCs > 75%",
returnPlot = FALSE
)
ploadings <- plotloadings(p,
rangeRetain = 0.01, labSize = 3.5,
title = "Loadings plot", axisLabSize = 12,
subtitle = "PC1, PC2, PC3, PC4, PC5",
caption = "Top 1% variables",
shape = 23, shapeSizeRange = c(4, 4),
col = c("limegreen", "black", "red3"),
legendPosition = "none",
drawConnectors = FALSE,
returnPlot = FALSE
)## -- variables retained:
## Gm26825, Ldhc, RP23-79J21.2, Rpl15-ps3, n-R5s100, AC164158.1, RP23-8J15.3, Agpat2, St14, RP24-333C3.5, Obscn
library(cowplot)
library(ggplotify)
top_row <- plot_grid(pscree, ppairs, pbiplot,
ncol = 3,
labels = c("A", "B Pairs plot", "C"),
label_fontfamily = "serif",
label_fontface = "bold",
label_size = 22,
align = "h",
rel_widths = c(1.05, 0.9, 1.05)
)
bottom_row <- plot_grid(ploadings,
ncol = 1,
labels = c("D"),
label_fontfamily = "serif",
label_fontface = "bold",
label_size = 22,
align = "h",
rel_widths = c(1.5, 1.5)
)SessionInfo
## ─ Session info ──────────────────────────────────────────────────────────
## setting value
## version R version 3.5.3 (2019-03-11)
## os Ubuntu 16.04.6 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Zurich
## date 2019-06-18
##
## ─ Packages ──────────────────────────────────────────────────────────────
## package * version date lib
## acepack 1.4.1 2016-10-29 [1]
## annotate 1.60.1 2019-03-07 [1]
## AnnotationDbi 1.44.0 2018-10-30 [1]
## assertthat 0.2.1 2019-03-21 [1]
## autoplotly * 0.1.2 2018-04-21 [1]
## backports 1.1.4 2019-04-10 [1]
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## Biobase 2.42.0 2018-10-30 [1]
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## BiocParallel 1.16.6 2019-02-10 [1]
## Biostrings 2.50.2 2019-01-03 [1]
## bit 1.1-14 2018-05-29 [1]
## bit64 0.9-7 2017-05-08 [1]
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## blob 1.1.1 2018-03-25 [1]
## bookdown 0.11 2019-05-28 [1]
## Cairo 1.5-10 2019-03-28 [1]
## callr 3.2.0 2019-03-15 [1]
## checkmate 1.9.3 2019-05-03 [1]
## cli 1.1.0 2019-03-19 [1]
## cluster 2.0.9 2019-05-01 [1]
## colorspace 1.4-1 2019-03-18 [1]
## corrplot * 0.84 2017-10-16 [1]
## cowplot * 0.9.4 2019-01-08 [1]
## crayon 1.3.4 2017-09-16 [1]
## crosstalk 1.0.0 2016-12-21 [1]
## data.table 1.12.2 2019-04-07 [1]
## DBI 1.0.0 2018-05-02 [1]
## DelayedArray 0.8.0 2018-10-30 [1]
## dendextend * 1.12.0 2019-05-11 [1]
## desc 1.2.0 2018-05-01 [1]
## DESeq2 1.22.2 2019-01-04 [1]
## devtools * 2.0.2 2019-04-08 [1]
## digest 0.6.19 2019-05-20 [1]
## dplyr 0.8.1 2019-05-14 [1]
## edgeR 3.24.3 2019-01-02 [1]
## evaluate 0.14 2019-05-28 [1]
## foreign 0.8-71 2018-07-20 [1]
## Formula 1.2-3 2018-05-03 [1]
## fs 1.3.1 2019-05-06 [1]
## genefilter 1.64.0 2018-10-30 [1]
## geneplotter 1.60.0 2018-10-30 [1]
## GenomeInfoDb 1.18.2 2019-02-12 [1]
## GenomeInfoDbData 1.2.0 2019-01-17 [1]
## GenomicRanges 1.34.0 2018-10-30 [1]
## GEOquery 2.50.5 2018-12-22 [1]
## ggfortify * 0.4.7 2019-05-26 [1]
## ggplot2 * 3.1.1 2019-04-07 [1]
## ggplotify * 0.0.3 2018-08-03 [1]
## ggrepel * 0.8.1 2019-05-07 [1]
## glue 1.3.1 2019-03-12 [1]
## gridExtra 2.3 2017-09-09 [1]
## gridGraphics 0.4-1 2019-05-20 [1]
## gtable 0.3.0 2019-03-25 [1]
## highr 0.8 2019-03-20 [1]
## Hmisc 4.2-0 2019-01-26 [1]
## hms 0.4.2 2018-03-10 [1]
## htmlTable 1.13.1 2019-01-07 [1]
## htmltools 0.3.6 2017-04-28 [1]
## htmlwidgets 1.3 2018-09-30 [1]
## httpuv 1.5.1 2019-04-05 [1]
## httr 1.4.0 2018-12-11 [1]
## IRanges 2.16.0 2018-10-30 [1]
## jsonlite 1.6 2018-12-07 [1]
## knitr 1.23 2019-05-18 [1]
## labeling 0.3 2014-08-23 [1]
## later 0.8.0 2019-02-11 [1]
## lattice * 0.20-38 2018-11-04 [1]
## latticeExtra 0.6-28 2016-02-09 [1]
## lazyeval 0.2.2 2019-03-15 [1]
## limma * 3.38.3 2018-12-02 [1]
## locfit 1.5-9.1 2013-04-20 [1]
## magrittr 1.5 2014-11-22 [1]
## Matrix 1.2-17 2019-03-22 [1]
## matrixStats 0.54.0 2018-07-23 [1]
## memoise 1.1.0 2017-04-21 [1]
## mime 0.7 2019-06-11 [1]
## miniUI 0.1.1.1 2018-05-18 [1]
## munsell 0.5.0 2018-06-12 [1]
## nnet 7.3-12 2016-02-02 [1]
## PCAtools * 0.99.13 2019-06-18 [1]
## pheatmap * 1.0.12 2019-01-04 [1]
## pillar 1.4.1 2019-05-28 [1]
## pkgbuild 1.0.3 2019-03-20 [1]
## pkgconfig 2.0.2 2018-08-16 [1]
## pkgload 1.0.2 2018-10-29 [1]
## plgINS * 0.1.5 2019-06-07 [1]
## plotly * 4.9.0 2019-04-10 [1]
## plyr 1.8.4 2016-06-08 [1]
## prettyunits 1.0.2 2015-07-13 [1]
## processx 3.3.1 2019-05-08 [1]
## promises 1.0.1 2018-04-13 [1]
## ps 1.3.0 2018-12-21 [1]
## purrr 0.3.2 2019-03-15 [1]
## questionr 0.7.0 2018-11-26 [1]
## R6 2.4.0 2019-02-14 [1]
## RColorBrewer * 1.1-2 2014-12-07 [1]
## Rcpp 1.0.1 2019-03-17 [1]
## RCurl 1.95-4.12 2019-03-04 [1]
## readr 1.3.1 2018-12-21 [1]
## remotes 2.0.4 2019-04-10 [1]
## reshape2 * 1.4.3 2017-12-11 [1]
## rlang 0.3.4 2019-04-07 [1]
## rmarkdown 1.13 2019-05-22 [1]
## rmdformats 0.3.5 2019-02-19 [1]
## rpart 4.1-15 2019-04-12 [1]
## rprojroot 1.3-2 2018-01-03 [1]
## RSQLite 2.1.1 2018-05-06 [1]
## rstudioapi 0.10 2019-03-19 [1]
## rvcheck 0.1.3 2018-12-06 [1]
## S4Vectors 0.20.1 2018-11-09 [1]
## scales 1.0.0 2018-08-09 [1]
## sessioninfo 1.1.1 2018-11-05 [1]
## shiny 1.3.2 2019-04-22 [1]
## SRAdb 1.44.0 2018-10-30 [1]
## stringi 1.4.3 2019-03-12 [1]
## stringr 1.4.0 2019-02-10 [1]
## SummarizedExperiment 1.12.0 2018-10-30 [1]
## survival 2.44-1.1 2019-04-01 [1]
## testthat 2.1.1 2019-04-23 [1]
## tibble 2.1.3 2019-06-06 [1]
## tidyr 0.8.3 2019-03-01 [1]
## tidyselect 0.2.5 2018-10-11 [1]
## usethis * 1.5.0 2019-04-07 [1]
## viridis * 0.5.1 2018-03-29 [1]
## viridisLite * 0.3.0 2018-02-01 [1]
## withr 2.1.2 2018-03-15 [1]
## xfun 0.7 2019-05-14 [1]
## XML 3.98-1.20 2019-06-06 [1]
## xml2 1.2.0 2018-01-24 [1]
## xtable 1.8-4 2019-04-21 [1]
## XVector 0.22.0 2018-10-30 [1]
## yaml 2.2.0 2018-07-25 [1]
## zlibbioc 1.28.0 2018-10-30 [1]
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